Starting phenix.real_space_refine on Sat Aug 8 11:13:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21uy_68019/08_2026/21uy_68019.cif Found real_map, /net/cci-nas-00/data/ceres_data/21uy_68019/08_2026/21uy_68019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21uy_68019/08_2026/21uy_68019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21uy_68019/08_2026/21uy_68019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21uy_68019/08_2026/21uy_68019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21uy_68019/08_2026/21uy_68019.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 17375 2.51 5 N 4600 2.21 5 O 5330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 190 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27385 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "N" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2597 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 15, 'TRANS': 315} Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "D" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2597 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 15, 'TRANS': 315} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "I" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "J" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "K" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2597 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 15, 'TRANS': 315} Chain: "L" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "M" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "P" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2597 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 15, 'TRANS': 315} Chain: "Q" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "R" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "S" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Link IDs: {'TRANS': 127} Chain: "T" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2597 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 15, 'TRANS': 315} Time building chain proxies: 6.41, per 1000 atoms: 0.23 Number of scatterers: 27385 At special positions: 0 Unit cell: (248.6, 255.2, 78.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 5330 8.00 N 4600 7.00 C 17375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6610 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 18.0% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 108 through 117 removed outlier: 3.554A pdb=" N ALA E 113 " --> pdb=" O ASP E 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 99 No H-bonds generated for 'chain 'F' and resid 97 through 99' Processing helix chain 'F' and resid 108 through 117 Processing helix chain 'G' and resid 97 through 99 No H-bonds generated for 'chain 'G' and resid 97 through 99' Processing helix chain 'G' and resid 108 through 117 Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.988A pdb=" N ASP N 91 " --> pdb=" O LYS N 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE N 92 " --> pdb=" O ALA N 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 88 through 92' Processing helix chain 'N' and resid 109 through 139 removed outlier: 3.823A pdb=" N VAL N 113 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN N 120 " --> pdb=" O ARG N 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA N 136 " --> pdb=" O ILE N 132 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL N 137 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 159 Processing helix chain 'N' and resid 176 through 193 removed outlier: 3.964A pdb=" N THR N 180 " --> pdb=" O SER N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 207 through 216 Processing helix chain 'N' and resid 230 through 238 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.554A pdb=" N ALA A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.988A pdb=" N ASP D 91 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing helix chain 'D' and resid 109 through 139 removed outlier: 3.823A pdb=" N VAL D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 136 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL D 137 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.964A pdb=" N THR D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 108 through 117 removed outlier: 3.554A pdb=" N ALA H 113 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 99 No H-bonds generated for 'chain 'I' and resid 97 through 99' Processing helix chain 'I' and resid 108 through 117 Processing helix chain 'J' and resid 97 through 99 No H-bonds generated for 'chain 'J' and resid 97 through 99' Processing helix chain 'J' and resid 108 through 117 Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 88 through 92 removed outlier: 3.988A pdb=" N ASP K 91 " --> pdb=" O LYS K 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE K 92 " --> pdb=" O ALA K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 88 through 92' Processing helix chain 'K' and resid 109 through 139 removed outlier: 3.823A pdb=" N VAL K 113 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS K 131 " --> pdb=" O LYS K 127 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL K 137 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 159 Processing helix chain 'K' and resid 176 through 193 removed outlier: 3.964A pdb=" N THR K 180 " --> pdb=" O SER K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 216 Processing helix chain 'K' and resid 230 through 238 Processing helix chain 'L' and resid 73 through 77 Processing helix chain 'L' and resid 97 through 99 No H-bonds generated for 'chain 'L' and resid 97 through 99' Processing helix chain 'L' and resid 108 through 117 removed outlier: 3.553A pdb=" N ALA L 113 " --> pdb=" O ASP L 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 99 No H-bonds generated for 'chain 'M' and resid 97 through 99' Processing helix chain 'M' and resid 108 through 117 Processing helix chain 'O' and resid 97 through 99 No H-bonds generated for 'chain 'O' and resid 97 through 99' Processing helix chain 'O' and resid 108 through 117 Processing helix chain 'P' and resid 24 through 29 Processing helix chain 'P' and resid 88 through 92 removed outlier: 3.987A pdb=" N ASP P 91 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE P 92 " --> pdb=" O ALA P 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 88 through 92' Processing helix chain 'P' and resid 109 through 139 removed outlier: 3.823A pdb=" N VAL P 113 " --> pdb=" O THR P 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN P 120 " --> pdb=" O ARG P 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS P 131 " --> pdb=" O LYS P 127 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA P 136 " --> pdb=" O ILE P 132 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL P 137 " --> pdb=" O PHE P 133 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET P 138 " --> pdb=" O ALA P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 154 through 159 Processing helix chain 'P' and resid 176 through 193 removed outlier: 3.963A pdb=" N THR P 180 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 216 Processing helix chain 'P' and resid 230 through 238 Processing helix chain 'Q' and resid 73 through 77 Processing helix chain 'Q' and resid 97 through 99 No H-bonds generated for 'chain 'Q' and resid 97 through 99' Processing helix chain 'Q' and resid 108 through 117 removed outlier: 3.554A pdb=" N ALA Q 113 " --> pdb=" O ASP Q 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 99 No H-bonds generated for 'chain 'R' and resid 97 through 99' Processing helix chain 'R' and resid 108 through 117 Processing helix chain 'S' and resid 97 through 99 No H-bonds generated for 'chain 'S' and resid 97 through 99' Processing helix chain 'S' and resid 108 through 117 Processing helix chain 'T' and resid 24 through 29 Processing helix chain 'T' and resid 88 through 92 removed outlier: 3.988A pdb=" N ASP T 91 " --> pdb=" O LYS T 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE T 92 " --> pdb=" O ALA T 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 88 through 92' Processing helix chain 'T' and resid 109 through 139 removed outlier: 3.823A pdb=" N VAL T 113 " --> pdb=" O THR T 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN T 120 " --> pdb=" O ARG T 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS T 131 " --> pdb=" O LYS T 127 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA T 136 " --> pdb=" O ILE T 132 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL T 137 " --> pdb=" O PHE T 133 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET T 138 " --> pdb=" O ALA T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 154 through 159 Processing helix chain 'T' and resid 176 through 193 removed outlier: 3.964A pdb=" N THR T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 207 through 216 Processing helix chain 'T' and resid 230 through 238 Processing sheet with id=1, first strand: chain 'E' and resid 31 through 37 removed outlier: 3.623A pdb=" N TRP E 67 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU E 65 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'E' and resid 93 through 95 Processing sheet with id=3, first strand: chain 'F' and resid 31 through 37 removed outlier: 3.517A pdb=" N VAL F 34 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR F 84 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR F 68 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL F 86 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL F 64 " --> pdb=" O GLY F 88 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 63 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'F' and resid 93 through 95 removed outlier: 6.855A pdb=" N LEU F 94 " --> pdb=" O THR F 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=4 Processing sheet with id=5, first strand: chain 'G' and resid 18 through 21 removed outlier: 4.138A pdb=" N THR G 93 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'G' and resid 31 through 37 removed outlier: 3.514A pdb=" N VAL G 34 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP G 67 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU G 65 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.988A pdb=" N ASP N 33 " --> pdb=" O ALA N 280 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR N 282 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLN N 35 " --> pdb=" O TYR N 282 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'N' and resid 41 through 46 removed outlier: 3.626A pdb=" N ILE N 42 " --> pdb=" O PHE N 76 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG N 46 " --> pdb=" O SER N 72 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER N 72 " --> pdb=" O ARG N 46 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'N' and resid 81 through 87 Processing sheet with id=10, first strand: chain 'N' and resid 165 through 168 removed outlier: 6.278A pdb=" N VAL N 166 " --> pdb=" O THR N 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL N 252 " --> pdb=" O TRP N 249 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 31 through 37 removed outlier: 3.623A pdb=" N TRP A 67 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 65 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=13, first strand: chain 'B' and resid 31 through 37 removed outlier: 3.517A pdb=" N VAL B 34 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR B 84 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR B 68 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 86 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 64 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 63 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.855A pdb=" N LEU B 94 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'C' and resid 18 through 21 removed outlier: 4.139A pdb=" N THR C 93 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 31 through 37 removed outlier: 3.514A pdb=" N VAL C 34 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 67 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 65 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 33 through 36 removed outlier: 5.988A pdb=" N ASP D 33 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR D 282 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLN D 35 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 41 through 46 removed outlier: 3.626A pdb=" N ILE D 42 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 46 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER D 72 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 81 through 87 Processing sheet with id=20, first strand: chain 'D' and resid 165 through 168 removed outlier: 6.277A pdb=" N VAL D 166 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 252 " --> pdb=" O TRP D 249 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'H' and resid 31 through 37 removed outlier: 3.623A pdb=" N TRP H 67 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU H 65 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'H' and resid 93 through 95 Processing sheet with id=23, first strand: chain 'I' and resid 31 through 37 removed outlier: 3.517A pdb=" N VAL I 34 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR I 84 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR I 68 " --> pdb=" O THR I 84 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL I 86 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL I 64 " --> pdb=" O GLY I 88 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS I 63 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 93 through 95 removed outlier: 6.855A pdb=" N LEU I 94 " --> pdb=" O THR I 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=24 Processing sheet with id=25, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.138A pdb=" N THR J 93 " --> pdb=" O LEU J 19 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'J' and resid 31 through 37 removed outlier: 3.514A pdb=" N VAL J 34 " --> pdb=" O ALA J 85 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP J 67 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY J 88 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU J 65 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 33 through 36 removed outlier: 5.987A pdb=" N ASP K 33 " --> pdb=" O ALA K 280 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR K 282 " --> pdb=" O ASP K 33 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLN K 35 " --> pdb=" O TYR K 282 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.626A pdb=" N ILE K 42 " --> pdb=" O PHE K 76 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG K 46 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER K 72 " --> pdb=" O ARG K 46 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'K' and resid 81 through 87 Processing sheet with id=30, first strand: chain 'K' and resid 165 through 168 removed outlier: 6.278A pdb=" N VAL K 166 " --> pdb=" O THR K 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL K 252 " --> pdb=" O TRP K 249 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'L' and resid 31 through 37 removed outlier: 3.623A pdb=" N TRP L 67 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY L 88 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 65 " --> pdb=" O GLY L 88 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'L' and resid 93 through 95 Processing sheet with id=33, first strand: chain 'M' and resid 31 through 37 removed outlier: 3.517A pdb=" N VAL M 34 " --> pdb=" O ALA M 85 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR M 84 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR M 68 " --> pdb=" O THR M 84 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL M 86 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL M 64 " --> pdb=" O GLY M 88 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS M 63 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'M' and resid 93 through 95 removed outlier: 6.856A pdb=" N LEU M 94 " --> pdb=" O THR M 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=34 Processing sheet with id=35, first strand: chain 'O' and resid 18 through 21 removed outlier: 4.138A pdb=" N THR O 93 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'O' and resid 31 through 37 removed outlier: 3.514A pdb=" N VAL O 34 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP O 67 " --> pdb=" O VAL O 86 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY O 88 " --> pdb=" O LEU O 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU O 65 " --> pdb=" O GLY O 88 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'P' and resid 33 through 36 removed outlier: 5.987A pdb=" N ASP P 33 " --> pdb=" O ALA P 280 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR P 282 " --> pdb=" O ASP P 33 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN P 35 " --> pdb=" O TYR P 282 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'P' and resid 41 through 46 removed outlier: 3.626A pdb=" N ILE P 42 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG P 46 " --> pdb=" O SER P 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER P 72 " --> pdb=" O ARG P 46 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'P' and resid 81 through 87 Processing sheet with id=40, first strand: chain 'P' and resid 165 through 168 removed outlier: 6.277A pdb=" N VAL P 166 " --> pdb=" O THR P 331 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL P 252 " --> pdb=" O TRP P 249 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'Q' and resid 31 through 37 removed outlier: 3.623A pdb=" N TRP Q 67 " --> pdb=" O VAL Q 86 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY Q 88 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU Q 65 " --> pdb=" O GLY Q 88 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'Q' and resid 93 through 95 Processing sheet with id=43, first strand: chain 'R' and resid 31 through 37 removed outlier: 3.517A pdb=" N VAL R 34 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR R 84 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR R 68 " --> pdb=" O THR R 84 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL R 86 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL R 64 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS R 63 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'R' and resid 93 through 95 removed outlier: 6.855A pdb=" N LEU R 94 " --> pdb=" O THR R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=44 Processing sheet with id=45, first strand: chain 'S' and resid 18 through 21 removed outlier: 4.139A pdb=" N THR S 93 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'S' and resid 31 through 37 removed outlier: 3.514A pdb=" N VAL S 34 " --> pdb=" O ALA S 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP S 67 " --> pdb=" O VAL S 86 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY S 88 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU S 65 " --> pdb=" O GLY S 88 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'T' and resid 33 through 36 removed outlier: 5.988A pdb=" N ASP T 33 " --> pdb=" O ALA T 280 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR T 282 " --> pdb=" O ASP T 33 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLN T 35 " --> pdb=" O TYR T 282 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'T' and resid 41 through 46 removed outlier: 3.625A pdb=" N ILE T 42 " --> pdb=" O PHE T 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG T 46 " --> pdb=" O SER T 72 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER T 72 " --> pdb=" O ARG T 46 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'T' and resid 81 through 87 Processing sheet with id=50, first strand: chain 'T' and resid 165 through 168 removed outlier: 6.278A pdb=" N VAL T 166 " --> pdb=" O THR T 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL T 252 " --> pdb=" O TRP T 249 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9057 1.34 - 1.46: 4557 1.46 - 1.57: 14096 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 27850 Sorted by residual: bond pdb=" N LYS R 49 " pdb=" CA LYS R 49 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.17e-02 7.31e+03 8.22e+00 bond pdb=" N LYS F 49 " pdb=" CA LYS F 49 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 8.00e+00 bond pdb=" N LYS I 49 " pdb=" CA LYS I 49 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N LYS M 49 " pdb=" CA LYS M 49 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.86e+00 bond pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.84e+00 ... (remaining 27845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 36810 1.83 - 3.66: 949 3.66 - 5.50: 61 5.50 - 7.33: 5 7.33 - 9.16: 20 Bond angle restraints: 37845 Sorted by residual: angle pdb=" C MET K 242 " pdb=" N ASP K 243 " pdb=" CA ASP K 243 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C MET D 242 " pdb=" N ASP D 243 " pdb=" CA ASP D 243 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C MET N 242 " pdb=" N ASP N 243 " pdb=" CA ASP N 243 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C MET T 242 " pdb=" N ASP T 243 " pdb=" CA ASP T 243 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C MET P 242 " pdb=" N ASP P 243 " pdb=" CA ASP P 243 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 ... (remaining 37840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 14295 16.45 - 32.90: 1599 32.90 - 49.36: 446 49.36 - 65.81: 60 65.81 - 82.26: 35 Dihedral angle restraints: 16435 sinusoidal: 6155 harmonic: 10280 Sorted by residual: dihedral pdb=" CA GLN C 12 " pdb=" C GLN C 12 " pdb=" N GLU C 13 " pdb=" CA GLU C 13 " ideal model delta harmonic sigma weight residual 180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN S 12 " pdb=" C GLN S 12 " pdb=" N GLU S 13 " pdb=" CA GLU S 13 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLN G 12 " pdb=" C GLN G 12 " pdb=" N GLU G 13 " pdb=" CA GLU G 13 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 16432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2416 0.026 - 0.053: 1170 0.053 - 0.079: 445 0.079 - 0.105: 270 0.105 - 0.131: 189 Chirality restraints: 4490 Sorted by residual: chirality pdb=" CA ILE P 78 " pdb=" N ILE P 78 " pdb=" C ILE P 78 " pdb=" CB ILE P 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE N 78 " pdb=" N ILE N 78 " pdb=" C ILE N 78 " pdb=" CB ILE N 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE D 78 " pdb=" N ILE D 78 " pdb=" C ILE D 78 " pdb=" CB ILE D 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 4487 not shown) Planarity restraints: 4865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 54 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO N 55 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO N 55 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 55 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE T 54 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO T 55 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO T 55 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO T 55 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 54 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO K 55 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO K 55 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 55 " 0.040 5.00e-02 4.00e+02 ... (remaining 4862 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 65 2.42 - 3.04: 14942 3.04 - 3.66: 34649 3.66 - 4.28: 49819 4.28 - 4.90: 90309 Nonbonded interactions: 189784 Sorted by model distance: nonbonded pdb=" O ALA P 199 " pdb=" O ASN T 241 " model vdw 1.797 3.040 nonbonded pdb=" O ALA K 199 " pdb=" O ASN P 241 " model vdw 1.798 3.040 nonbonded pdb=" O ALA D 199 " pdb=" O ASN K 241 " model vdw 1.798 3.040 nonbonded pdb=" O ALA N 199 " pdb=" O ASN D 241 " model vdw 1.798 3.040 nonbonded pdb=" O ASN N 241 " pdb=" O ALA T 199 " model vdw 1.798 3.040 ... (remaining 189779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.410 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 27850 Z= 0.238 Angle : 0.703 9.161 37845 Z= 0.425 Chirality : 0.044 0.131 4490 Planarity : 0.005 0.072 4865 Dihedral : 15.305 82.262 9825 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.67 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 3535 helix: -0.28 (0.21), residues: 500 sheet: 0.17 (0.20), residues: 685 loop : -1.81 (0.10), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 59 TYR 0.010 0.001 TYR P 224 PHE 0.024 0.002 PHE Q 14 TRP 0.012 0.002 TRP I 67 HIS 0.006 0.001 HIS J 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.24 (27850) covalent geometry : angle 0.70270 / 0.43 (37845) hydrogen bonds : bond 0.27849 / 18.93 ( 675) hydrogen bonds : angle 7.55512 / 5.23 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.024 Fit side-chains REVERT: F 116 GLU cc_start: 0.8510 (tp30) cc_final: 0.8269 (tp30) REVERT: K 15 MET cc_start: 0.8679 (mtm) cc_final: 0.8370 (mtp) REVERT: M 75 ASP cc_start: 0.7947 (m-30) cc_final: 0.7580 (m-30) REVERT: O 76 ASP cc_start: 0.8136 (m-30) cc_final: 0.7882 (m-30) REVERT: P 84 ASP cc_start: 0.7656 (p0) cc_final: 0.7446 (p0) REVERT: T 15 MET cc_start: 0.8654 (mtm) cc_final: 0.8399 (mtp) REVERT: T 84 ASP cc_start: 0.7595 (p0) cc_final: 0.7343 (p0) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.6334 time to fit residues: 279.1020 Evaluate side-chains 330 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.0070 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 245 GLN C 95 ASN D 245 GLN I 35 ASN J 95 ASN K 241 ASN K 245 GLN M 35 ASN O 35 ASN O 95 ASN P 245 GLN S 35 ASN T 8 GLN T 241 ASN T 245 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111502 restraints weight = 36647.827| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.62 r_work: 0.3155 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27850 Z= 0.200 Angle : 0.671 10.215 37845 Z= 0.373 Chirality : 0.047 0.153 4490 Planarity : 0.006 0.073 4865 Dihedral : 5.381 28.818 3825 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.88 % Favored : 93.69 % Rotamer: Outliers : 3.60 % Allowed : 16.64 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.12), residues: 3535 helix: 0.25 (0.22), residues: 505 sheet: -0.06 (0.20), residues: 680 loop : -1.91 (0.10), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 46 TYR 0.014 0.002 TYR Q 97 PHE 0.022 0.002 PHE N 80 TRP 0.013 0.002 TRP F 67 HIS 0.008 0.002 HIS S 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (27850) covalent geometry : angle 0.67129 / 0.37 (37845) hydrogen bonds : bond 0.07911 / 5.46 ( 675) hydrogen bonds : angle 6.10024 / 4.21 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 352 time to evaluate : 1.073 Fit side-chains REVERT: E 116 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: F 116 GLU cc_start: 0.8634 (tp30) cc_final: 0.8387 (tp30) REVERT: B 16 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7266 (m-70) REVERT: B 27 LEU cc_start: 0.7897 (mp) cc_final: 0.7674 (mt) REVERT: D 296 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8130 (mtm-85) REVERT: H 116 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: H 124 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: J 129 THR cc_start: 0.8344 (t) cc_final: 0.8071 (m) REVERT: K 15 MET cc_start: 0.8717 (mtm) cc_final: 0.8380 (mtp) REVERT: M 75 ASP cc_start: 0.8746 (m-30) cc_final: 0.8311 (m-30) REVERT: S 129 THR cc_start: 0.8066 (t) cc_final: 0.7855 (m) REVERT: T 15 MET cc_start: 0.8682 (mtm) cc_final: 0.8448 (mtp) REVERT: T 225 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8131 (tt0) outliers start: 105 outliers final: 43 residues processed: 414 average time/residue: 0.5760 time to fit residues: 283.6130 Evaluate side-chains 369 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 320 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 225 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 143 optimal weight: 9.9990 chunk 231 optimal weight: 0.0970 chunk 172 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 294 optimal weight: 0.0570 chunk 125 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 overall best weight: 1.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN A 95 ASN C 95 ASN D 8 GLN H 95 ASN J 95 ASN L 95 ASN M 35 ASN O 35 ASN O 95 ASN Q 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115944 restraints weight = 36923.019| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.42 r_work: 0.3220 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27850 Z= 0.150 Angle : 0.575 10.215 37845 Z= 0.319 Chirality : 0.044 0.131 4490 Planarity : 0.005 0.068 4865 Dihedral : 4.985 26.703 3825 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.61 % Favored : 94.96 % Rotamer: Outliers : 3.32 % Allowed : 17.77 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 3535 helix: 0.48 (0.22), residues: 505 sheet: 0.08 (0.20), residues: 670 loop : -1.88 (0.10), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 59 TYR 0.009 0.001 TYR T 117 PHE 0.014 0.001 PHE D 80 TRP 0.012 0.001 TRP F 67 HIS 0.005 0.001 HIS S 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (27850) covalent geometry : angle 0.57486 / 0.32 (37845) hydrogen bonds : bond 0.06361 / 4.38 ( 675) hydrogen bonds : angle 5.79927 / 4.00 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 324 time to evaluate : 1.158 Fit side-chains REVERT: E 116 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: F 116 GLU cc_start: 0.8807 (tp30) cc_final: 0.8578 (tp30) REVERT: G 6 SER cc_start: 0.9345 (p) cc_final: 0.8974 (t) REVERT: C 16 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.7923 (m-70) REVERT: H 19 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7482 (pp) REVERT: J 129 THR cc_start: 0.8288 (t) cc_final: 0.8009 (m) REVERT: K 15 MET cc_start: 0.8670 (mtm) cc_final: 0.8344 (mtp) REVERT: L 116 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: M 75 ASP cc_start: 0.8778 (m-30) cc_final: 0.8373 (m-30) REVERT: P 233 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7463 (mp) outliers start: 97 outliers final: 50 residues processed: 388 average time/residue: 0.5805 time to fit residues: 267.7789 Evaluate side-chains 363 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 233 LEU Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 152 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 340 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 320 optimal weight: 0.8980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN C 95 ASN J 95 ASN M 35 ASN O 35 ASN O 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109608 restraints weight = 36886.119| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.48 r_work: 0.3119 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27850 Z= 0.228 Angle : 0.708 11.147 37845 Z= 0.391 Chirality : 0.048 0.156 4490 Planarity : 0.006 0.077 4865 Dihedral : 5.516 29.840 3825 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.70 % Favored : 92.87 % Rotamer: Outliers : 4.59 % Allowed : 16.75 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.12), residues: 3535 helix: 0.36 (0.22), residues: 505 sheet: -0.06 (0.19), residues: 675 loop : -2.15 (0.10), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 59 TYR 0.013 0.002 TYR Q 97 PHE 0.020 0.002 PHE D 80 TRP 0.013 0.002 TRP F 67 HIS 0.009 0.002 HIS S 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (27850) covalent geometry : angle 0.70769 / 0.39 (37845) hydrogen bonds : bond 0.08462 / 5.86 ( 675) hydrogen bonds : angle 5.98747 / 4.13 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 310 time to evaluate : 1.082 Fit side-chains REVERT: F 19 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7515 (pp) REVERT: F 116 GLU cc_start: 0.8725 (tp30) cc_final: 0.8509 (tp30) REVERT: G 19 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7061 (pp) REVERT: B 19 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7366 (pp) REVERT: C 16 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.7934 (m-70) REVERT: C 75 ASP cc_start: 0.9179 (m-30) cc_final: 0.8791 (m-30) REVERT: H 19 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7494 (pp) REVERT: H 116 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: I 19 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7680 (pp) REVERT: I 75 ASP cc_start: 0.8558 (m-30) cc_final: 0.8083 (m-30) REVERT: I 105 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: J 102 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8361 (ttpp) REVERT: L 42 MET cc_start: 0.8692 (mtt) cc_final: 0.8427 (ttp) REVERT: M 19 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7420 (pp) REVERT: M 75 ASP cc_start: 0.8889 (m-30) cc_final: 0.8505 (m-30) REVERT: O 76 ASP cc_start: 0.8525 (m-30) cc_final: 0.8198 (m-30) REVERT: P 233 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7479 (mp) REVERT: P 242 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7131 (mmm) REVERT: Q 95 ASN cc_start: 0.8930 (t0) cc_final: 0.8710 (t0) REVERT: R 116 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8333 (tp30) outliers start: 134 outliers final: 71 residues processed: 405 average time/residue: 0.5965 time to fit residues: 285.4949 Evaluate side-chains 381 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 297 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 233 LEU Chi-restraints excluded: chain P residue 242 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 116 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 225 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 15 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 338 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 325 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN A 95 ASN H 95 ASN J 95 ASN M 35 ASN P 115 ASN S 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111700 restraints weight = 36699.429| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.47 r_work: 0.3146 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27850 Z= 0.178 Angle : 0.622 8.907 37845 Z= 0.346 Chirality : 0.045 0.153 4490 Planarity : 0.005 0.073 4865 Dihedral : 5.270 28.993 3825 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.49 % Favored : 94.09 % Rotamer: Outliers : 4.42 % Allowed : 17.29 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 3535 helix: 0.41 (0.22), residues: 505 sheet: -0.04 (0.19), residues: 730 loop : -2.13 (0.11), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 59 TYR 0.010 0.001 TYR T 117 PHE 0.015 0.002 PHE N 80 TRP 0.014 0.002 TRP F 67 HIS 0.007 0.001 HIS S 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (27850) covalent geometry : angle 0.62248 / 0.35 (37845) hydrogen bonds : bond 0.07155 / 4.95 ( 675) hydrogen bonds : angle 5.84914 / 4.03 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 301 time to evaluate : 0.716 Fit side-chains REVERT: F 19 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7536 (pp) REVERT: F 116 GLU cc_start: 0.8709 (tp30) cc_final: 0.8494 (tp30) REVERT: G 6 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8917 (t) REVERT: G 19 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7035 (pp) REVERT: B 19 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7340 (pp) REVERT: B 51 ASP cc_start: 0.7601 (m-30) cc_final: 0.7388 (m-30) REVERT: C 16 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8079 (m-70) REVERT: C 75 ASP cc_start: 0.9147 (m-30) cc_final: 0.8745 (m-30) REVERT: H 19 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7438 (pp) REVERT: H 116 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: I 19 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7718 (pp) REVERT: I 75 ASP cc_start: 0.8570 (m-30) cc_final: 0.8121 (m-30) REVERT: I 105 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8536 (m-30) REVERT: J 102 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8358 (tppp) REVERT: L 116 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: M 19 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7454 (pp) REVERT: M 75 ASP cc_start: 0.8817 (m-30) cc_final: 0.8449 (m-30) REVERT: O 76 ASP cc_start: 0.8556 (m-30) cc_final: 0.8257 (m-30) REVERT: P 233 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7512 (mp) REVERT: P 242 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6723 (mmm) REVERT: R 116 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8341 (tp30) outliers start: 129 outliers final: 76 residues processed: 393 average time/residue: 0.4709 time to fit residues: 220.1605 Evaluate side-chains 391 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 300 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 16 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 242 MET Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 233 LEU Chi-restraints excluded: chain P residue 242 MET Chi-restraints excluded: chain Q residue 16 HIS Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 116 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 225 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 248 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN C 95 ASN D 306 HIS H 95 ASN J 95 ASN K 306 HIS M 35 ASN P 115 ASN P 241 ASN Q 95 ASN S 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107120 restraints weight = 37363.042| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.36 r_work: 0.3106 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27850 Z= 0.270 Angle : 0.766 8.117 37845 Z= 0.422 Chirality : 0.050 0.169 4490 Planarity : 0.006 0.083 4865 Dihedral : 5.762 31.065 3825 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.98 % Favored : 91.60 % Rotamer: Outliers : 4.79 % Allowed : 17.29 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.12), residues: 3535 helix: 0.23 (0.22), residues: 505 sheet: -0.12 (0.19), residues: 675 loop : -2.39 (0.10), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 59 TYR 0.014 0.002 TYR O 97 PHE 0.020 0.002 PHE N 80 TRP 0.014 0.002 TRP F 67 HIS 0.011 0.002 HIS S 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.27 (27850) covalent geometry : angle 0.76561 / 0.42 (37845) hydrogen bonds : bond 0.09236 / 6.39 ( 675) hydrogen bonds : angle 6.06415 / 4.17 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 312 time to evaluate : 1.051 Fit side-chains REVERT: F 19 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7685 (pp) REVERT: F 116 GLU cc_start: 0.8811 (tp30) cc_final: 0.8595 (tp30) REVERT: G 19 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7037 (pp) REVERT: A 95 ASN cc_start: 0.8932 (t0) cc_final: 0.8653 (t0) REVERT: B 19 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7698 (pp) REVERT: B 51 ASP cc_start: 0.7711 (m-30) cc_final: 0.7491 (m-30) REVERT: C 75 ASP cc_start: 0.9252 (m-30) cc_final: 0.8856 (m-30) REVERT: H 19 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7605 (pp) REVERT: H 116 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: I 19 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7751 (pp) REVERT: I 75 ASP cc_start: 0.8702 (m-30) cc_final: 0.8234 (m-30) REVERT: I 105 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8573 (m-30) REVERT: J 102 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8438 (ttpp) REVERT: M 19 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7702 (pp) REVERT: M 75 ASP cc_start: 0.8864 (m-30) cc_final: 0.8492 (m-30) REVERT: P 233 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7701 (mp) REVERT: P 242 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7298 (mmm) REVERT: Q 16 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.8031 (t70) REVERT: R 116 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8469 (tp30) outliers start: 140 outliers final: 87 residues processed: 417 average time/residue: 0.5635 time to fit residues: 280.0666 Evaluate side-chains 405 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 305 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 16 HIS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 221 ARG Chi-restraints excluded: chain K residue 323 ARG Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 233 LEU Chi-restraints excluded: chain P residue 242 MET Chi-restraints excluded: chain Q residue 16 HIS Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 116 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 225 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 138 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 251 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN H 95 ASN J 95 ASN O 95 ASN P 115 ASN Q 95 ASN S 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108878 restraints weight = 36735.457| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.34 r_work: 0.3100 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 27850 Z= 0.250 Angle : 0.738 8.462 37845 Z= 0.409 Chirality : 0.049 0.173 4490 Planarity : 0.006 0.085 4865 Dihedral : 5.741 31.426 3825 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.87 % Favored : 92.70 % Rotamer: Outliers : 4.25 % Allowed : 18.63 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.12), residues: 3535 helix: 0.16 (0.22), residues: 505 sheet: -0.13 (0.19), residues: 725 loop : -2.45 (0.10), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 59 TYR 0.013 0.002 TYR P 299 PHE 0.018 0.002 PHE N 80 TRP 0.015 0.002 TRP F 67 HIS 0.010 0.002 HIS G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (27850) covalent geometry : angle 0.73821 / 0.41 (37845) hydrogen bonds : bond 0.08752 / 6.06 ( 675) hydrogen bonds : angle 6.05563 / 4.16 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 298 time to evaluate : 1.165 Fit side-chains REVERT: E 124 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: F 19 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7652 (pp) REVERT: F 116 GLU cc_start: 0.8810 (tp30) cc_final: 0.8605 (tp30) REVERT: G 19 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.6986 (pp) REVERT: B 16 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.7884 (m-70) REVERT: B 19 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7595 (pp) REVERT: B 51 ASP cc_start: 0.7726 (m-30) cc_final: 0.7513 (m-30) REVERT: C 75 ASP cc_start: 0.9230 (m-30) cc_final: 0.8836 (m-30) REVERT: D 105 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8525 (t0) REVERT: H 19 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7552 (pp) REVERT: H 96 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8165 (ttt-90) REVERT: H 116 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: I 19 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7791 (pp) REVERT: I 75 ASP cc_start: 0.8577 (m-30) cc_final: 0.8130 (m-30) REVERT: I 105 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8557 (m-30) REVERT: J 102 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8446 (ttpp) REVERT: M 19 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7816 (pp) REVERT: M 75 ASP cc_start: 0.8837 (m-30) cc_final: 0.8477 (m-30) REVERT: O 76 ASP cc_start: 0.8652 (m-30) cc_final: 0.8447 (m-30) REVERT: P 233 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7709 (mp) REVERT: P 242 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7292 (mmm) REVERT: R 51 ASP cc_start: 0.7820 (m-30) cc_final: 0.7590 (m-30) REVERT: R 116 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8468 (tp30) outliers start: 124 outliers final: 88 residues processed: 391 average time/residue: 0.5152 time to fit residues: 239.9018 Evaluate side-chains 398 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 294 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 16 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 221 ARG Chi-restraints excluded: chain K residue 323 ARG Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 233 LEU Chi-restraints excluded: chain P residue 242 MET Chi-restraints excluded: chain Q residue 16 HIS Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 116 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 225 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 221 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 270 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN A 95 ASN H 95 ASN J 95 ASN O 95 ASN P 115 ASN Q 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.113045 restraints weight = 36771.249| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.35 r_work: 0.3152 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27850 Z= 0.164 Angle : 0.603 8.231 37845 Z= 0.335 Chirality : 0.045 0.137 4490 Planarity : 0.005 0.075 4865 Dihedral : 5.259 29.094 3825 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.11 % Favored : 93.47 % Rotamer: Outliers : 4.04 % Allowed : 19.14 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 3535 helix: 0.36 (0.22), residues: 505 sheet: -0.02 (0.20), residues: 720 loop : -2.32 (0.11), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 59 TYR 0.009 0.001 TYR P 299 PHE 0.015 0.001 PHE D 315 TRP 0.013 0.002 TRP F 67 HIS 0.006 0.001 HIS G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (27850) covalent geometry : angle 0.60250 / 0.33 (37845) hydrogen bonds : bond 0.06738 / 4.66 ( 675) hydrogen bonds : angle 5.81373 / 4.00 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 301 time to evaluate : 0.842 Fit side-chains REVERT: F 19 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7572 (pp) REVERT: F 116 GLU cc_start: 0.8740 (tp30) cc_final: 0.8483 (tp30) REVERT: G 6 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8876 (t) REVERT: G 19 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.6984 (pp) REVERT: B 16 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.8057 (m-70) REVERT: B 19 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7616 (pp) REVERT: C 75 ASP cc_start: 0.9183 (m-30) cc_final: 0.8792 (m-30) REVERT: D 105 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8372 (t0) REVERT: H 116 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: I 16 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8090 (m-70) REVERT: I 19 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7778 (pp) REVERT: J 102 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8407 (tppp) REVERT: L 116 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: M 19 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7698 (pp) REVERT: M 75 ASP cc_start: 0.8783 (m-30) cc_final: 0.8501 (m-30) REVERT: O 76 ASP cc_start: 0.8671 (m-30) cc_final: 0.8463 (m-30) REVERT: P 242 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7203 (mmm) REVERT: R 116 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8422 (tp30) outliers start: 118 outliers final: 78 residues processed: 393 average time/residue: 0.5696 time to fit residues: 264.9933 Evaluate side-chains 385 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 293 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 16 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 221 ARG Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain K residue 323 ARG Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 242 MET Chi-restraints excluded: chain Q residue 16 HIS Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 116 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 299 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 311 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 262 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 212 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN C 95 ASN H 95 ASN J 95 ASN K 8 GLN O 35 ASN P 8 GLN Q 95 ASN S 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.118950 restraints weight = 36651.684| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.44 r_work: 0.3247 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27850 Z= 0.112 Angle : 0.507 8.425 37845 Z= 0.277 Chirality : 0.043 0.131 4490 Planarity : 0.004 0.061 4865 Dihedral : 4.551 24.300 3825 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.65 % Favored : 95.93 % Rotamer: Outliers : 2.60 % Allowed : 20.86 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.13), residues: 3535 helix: 0.53 (0.22), residues: 535 sheet: -0.06 (0.19), residues: 740 loop : -2.06 (0.11), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 208 TYR 0.007 0.001 TYR N 254 PHE 0.014 0.001 PHE P 315 TRP 0.009 0.001 TRP F 67 HIS 0.002 0.000 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.11 (27850) covalent geometry : angle 0.50664 / 0.28 (37845) hydrogen bonds : bond 0.04415 / 3.02 ( 675) hydrogen bonds : angle 5.42387 / 3.72 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 323 time to evaluate : 1.058 Fit side-chains REVERT: F 19 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7627 (pp) REVERT: F 116 GLU cc_start: 0.8634 (tp30) cc_final: 0.8390 (tp30) REVERT: G 6 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.8963 (t) REVERT: G 19 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7140 (pp) REVERT: B 16 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.6863 (m-70) REVERT: B 19 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7707 (pp) REVERT: C 75 ASP cc_start: 0.9083 (m-30) cc_final: 0.8672 (m-30) REVERT: H 19 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7443 (pp) REVERT: H 116 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: I 19 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7777 (pp) REVERT: L 116 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: M 19 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7627 (pp) REVERT: M 75 ASP cc_start: 0.8686 (m-30) cc_final: 0.8407 (m-30) REVERT: O 76 ASP cc_start: 0.8646 (m-30) cc_final: 0.8319 (m-30) REVERT: P 242 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7111 (mmm) outliers start: 76 outliers final: 31 residues processed: 386 average time/residue: 0.5472 time to fit residues: 250.4311 Evaluate side-chains 336 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 242 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain T residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 210 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 164 optimal weight: 0.0040 chunk 161 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 35 ASN G 35 ASN C 95 ASN M 35 ASN R 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114235 restraints weight = 36714.705| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.34 r_work: 0.3167 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27850 Z= 0.153 Angle : 0.584 9.400 37845 Z= 0.320 Chirality : 0.044 0.154 4490 Planarity : 0.004 0.063 4865 Dihedral : 4.877 26.936 3825 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.17 % Favored : 93.44 % Rotamer: Outliers : 2.29 % Allowed : 21.61 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.13), residues: 3535 helix: 0.76 (0.23), residues: 505 sheet: 0.16 (0.20), residues: 720 loop : -2.10 (0.11), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 59 TYR 0.009 0.001 TYR P 117 PHE 0.014 0.001 PHE N 80 TRP 0.011 0.001 TRP F 67 HIS 0.006 0.001 HIS S 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (27850) covalent geometry : angle 0.58376 / 0.32 (37845) hydrogen bonds : bond 0.06276 / 4.34 ( 675) hydrogen bonds : angle 5.51991 / 3.79 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7070 Ramachandran restraints generated. 3535 Oldfield, 0 Emsley, 3535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 1.070 Fit side-chains REVERT: E 19 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7897 (pp) REVERT: F 19 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7649 (pp) REVERT: F 116 GLU cc_start: 0.8727 (tp30) cc_final: 0.8487 (tp30) REVERT: G 6 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.8989 (t) REVERT: G 19 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7146 (pp) REVERT: B 19 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7742 (pp) REVERT: C 75 ASP cc_start: 0.9163 (m-30) cc_final: 0.8768 (m-30) REVERT: H 116 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: I 19 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7872 (pp) REVERT: M 19 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7718 (pp) REVERT: O 76 ASP cc_start: 0.8696 (m-30) cc_final: 0.8490 (m-30) REVERT: P 242 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7142 (mmm) outliers start: 67 outliers final: 45 residues processed: 346 average time/residue: 0.5359 time to fit residues: 218.8823 Evaluate side-chains 342 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 16 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 16 HIS Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 242 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 16 HIS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 16 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain T residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 259 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 233 optimal weight: 0.1980 chunk 181 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 277 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 ASN A 95 ASN C 95 ASN H 95 ASN L 95 ASN O 95 ASN Q 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116914 restraints weight = 36492.395| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.33 r_work: 0.3209 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27850 Z= 0.128 Angle : 0.539 8.996 37845 Z= 0.296 Chirality : 0.043 0.146 4490 Planarity : 0.004 0.061 4865 Dihedral : 4.679 23.843 3825 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.64 % Favored : 94.96 % Rotamer: Outliers : 2.23 % Allowed : 21.82 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3535 helix: 0.68 (0.22), residues: 535 sheet: 0.09 (0.19), residues: 735 loop : -2.02 (0.11), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 208 TYR 0.007 0.001 TYR N 254 PHE 0.014 0.001 PHE P 315 TRP 0.010 0.001 TRP F 67 HIS 0.004 0.001 HIS S 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (27850) covalent geometry : angle 0.53906 / 0.30 (37845) hydrogen bonds : bond 0.05333 / 3.67 ( 675) hydrogen bonds : angle 5.38999 / 3.71 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8298.05 seconds wall clock time: 141 minutes 55.29 seconds (8515.29 seconds total)